7QI8

CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.247 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Lysyl-tRNA synthetase, a target for urgently needed M. tuberculosis drugs.

Green, S.R.Davis, S.H.Damerow, S.Engelhart, C.A.Mathieson, M.Baragana, B.Robinson, D.A.Tamjar, J.Dawson, A.Tamaki, F.K.Buchanan, K.I.Post, J.Dowers, K.Shepherd, S.M.Jansen, C.Zuccotto, F.Gilbert, I.H.Epemolu, O.Riley, J.Stojanovski, L.Osuna-Cabello, M.Perez-Herran, E.Rebollo, M.J.Guijarro Lopez, L.Casado Castro, P.Camino, I.Kim, H.C.Bean, J.M.Nahiyaan, N.Rhee, K.Y.Wang, Q.Tan, V.Y.Boshoff, H.I.M.Converse, P.J.Li, S.Y.Chang, Y.S.Fotouhi, N.Upton, A.M.Nuermberger, E.L.Schnappinger, D.Read, K.D.Encinas, L.Bates, R.H.Wyatt, P.G.Cleghorn, L.A.T.

(2022) Nat Commun 13: 5992-5992

  • DOI: https://doi.org/10.1038/s41467-022-33736-5
  • Primary Citation of Related Structures:  
    7QH8, 7QHN, 7QI8

  • PubMed Abstract: 

    Tuberculosis is a major global cause of both mortality and financial burden mainly in low and middle-income countries. Given the significant and ongoing rise of drug-resistant strains of Mycobacterium tuberculosis within the clinical setting, there is an urgent need for the development of new, safe and effective treatments. Here the development of a drug-like series based on a fused dihydropyrrolidino-pyrimidine scaffold is described. The series has been developed against M. tuberculosis lysyl-tRNA synthetase (LysRS) and cellular studies support this mechanism of action. DDD02049209, the lead compound, is efficacious in mouse models of acute and chronic tuberculosis and has suitable physicochemical, pharmacokinetic properties and an in vitro safety profile that supports further development. Importantly, preliminary analysis using clinical resistant strains shows no pre-existing clinical resistance towards this scaffold.


  • Organizational Affiliation

    Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysine--tRNA ligase 1526Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: lysS1lysSRv3598cMTCY07H7B.24
EC: 6.1.1.6
UniProt
Find proteins for P9WFU9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WFU9 
Go to UniProtKB:  P9WFU9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WFU9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DD0
Query on DD0

Download Ideal Coordinates CCD File 
C [auth A]2-azanyl-6-[(1~{S},7~{S})-2,2-bis(fluoranyl)-7-oxidanyl-cycloheptyl]-4-methoxy-7~{H}-pyrrolo[3,4-d]pyrimidin-5-one
C14 H18 F2 N4 O3
VWSRMVWRUFUXMB-WPRPVWTQSA-N
LYS
Query on LYS

Download Ideal Coordinates CCD File 
B [auth A]LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.247 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.196α = 90
b = 84.196β = 90
c = 147.984γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesOPP1066891

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-19
    Type: Initial release
  • Version 1.1: 2023-05-31
    Changes: Database references, Source and taxonomy
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description